Publications

33 entries — 16 international journal, 1 international conference, 1 domestic journal, 15 domestic conference. 17 in SCIE-indexed venues.

† first author · * corresponding author

16 publications

2026

Integrative evidence-knowledge marker selection enhances LLM-based cell type annotation in single-cell RNA-seq analysis

Jiyeong Shin^{† (first author)}, Soyoung Jeong, Hyun Je Kim, Minsik Oh^{* (corresponding author)}

BioData Mining2026International journalSCIEIF 7.9

scFANCL: Dual contrastive learning with false-negative correction at cell level for single-cell RNA-seq clustering

Gunho Choi^{† (first author)}, Minsik Oh^{* (corresponding author)}

BMC Genomics2026International journalSCIEIF 3.9

Annotation-free phenotype prediction using knowledge-augmented clustering from single-cell RNA sequencing data

Janghyun Noh^{† (first author)}, Yoobin Shin, Min Kim, Minsik Oh^{* (corresponding author)}

Briefings in Bioinformatics2026International journalSCIEIF 7.3

Ferroptosis-based therapeutic strategy targeting iron metabolism and SLC7A11 overcomes oxaliplatin resistance in patient-derived pancreatic cancer organoids

Jin Ho Choi^{† (first author)}, Kyung Min Lee, Minsik Oh, Janghyun Noh, Yooyeon Kim, Eunhye Hwang, In Rae Cho, Woo Hyun Paik, Ji Kon Ryu, Ja-lok Ku, Sang Hyub Lee^{* (corresponding author)}

Journal of Experimental & Clinical Cancer Research2026International journalSCIEIF 14.3

2025

Integrative multi-omic profiling in blood reveals distinct immune and metabolic signatures between ACPA-negative and ACPA-positive rheumatoid arthritis

Benjamin Hur^{† (first author)}, Vinod K. Gupta, Minsik Oh, Hu Zeng, Cynthia S. Crowson, Kenneth J. Warrington, Elena Myasoedova, Vanessa L. Kronzer, John M. Davis, Jaeyun Sung^{* (corresponding author)}

Frontiers in Immunology2025International journalSCIEIF 7.0

Large DNA deletions occur during DNA repair at 20-fold lower frequency for base editors and prime editors than for Cas9 nucleases

Gue-Ho Hwang^{† (first author)}, Seok-Hoon Lee, Minsik Oh, Segi Kim, Omer Habib, Hyeon-Ki Jang, Heon Seok Kim, Youngkuk Kim, Chan Hyuk Kim, Sun Kim, Sangsu Bae^{* (corresponding author)}

Nature Biomedical Engineering2025International journalSCIEIF 26.3

2023

TFNetPropX: A web-based comprehensive analysis tool for exploring condition-specific RNA-seq data using transcription factor network propagation

Ji Hwan Moon^{† (first author)}, Minsik Oh^{* (corresponding author)}

Applied Sciences2023International journalSCIEIF 2.9

GOAT: Gene-level biomarker discovery from multi-omics data using graph ATtention neural network for eosinophilic asthma subtype

Dabin Jeong^{† (first author)}, Bonil Koo, Minsik Oh, Tae-Bum Kim^{* (corresponding author)}, Sun Kim^{* (corresponding author)}

Bioinformatics2023International journalSCIEIF 5.5

2022

Adipocyte HIF2α functions as a thermostat via PKA Cα regulation in beige adipocytes

Ji Seul Han^{† (first author)}, Yong Geun Jeon, Minsik Oh, Gung Lee, Hahn Nahmgoong, Sang Mun Han, Jeehye Choi, Ye Young Kim, Kyung Cheul Shin, Jiwon Kim, Kyuri Jo, Sung Sik Choe, Eun Jung Park, Sun Kim, Jae Bum Kim^{* (corresponding author)}

Nature Communications2022International journalSCIEIF 18.1

2021

mirTime: identifying condition-specific targets of microRNA in time-series transcript data using Gaussian process model and spherical vector clustering

Hyejin Kang^{† (first author)}, Hongryul Ahn, Kyuri Jo, Minsik Oh, Sun Kim^{* (corresponding author)}

Bioinformatics2021International journalSCIEIF 5.5

Construction of condition-specific gene regulatory network using kernel canonical correlation analysis

Dabin Jeong^{† (first author)}, Sangsoo Lim, Sangseon Lee, Minsik Oh, Changyun Cho, Hyeju Seong, Woosuk Jung, Sun Kim^{* (corresponding author)}

Frontiers in Genetics2021International journalSCIEIF 3.0

Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations

Minsik Oh^{† (first author)}, Sungjoon Park, Sun Kim, Heejoon Chae^{* (corresponding author)}

Briefings in Bioinformatics2021International journalSCIEIF 7.3

2020

DRIM: A web-based system for investigating drug response at the molecular level by condition-specific multi-omics data integration

Minsik Oh^{† (first author)}, Sungjoon Park, Sangseon Lee, Dohoon Lee, Sangsoo Lim, Dabin Jeong, Kyuri Jo, Inuk Jung, Sun Kim^{* (corresponding author)}

Frontiers in Genetics2020International journalSCIEIF 3.0

2018

DeepFam: deep learning based alignment-free method for protein family modeling and prediction

Seokjun Seo^{† (first author)}, Minsik Oh, Youngjune Park, Sun Kim^{* (corresponding author)}

Bioinformatics2018International journalSCIEIF 5.5

2017

miRTarVis+: Web-based interactive visual analytics tool for microRNA target predictions

Sehi L'Yi^{† (first author)}, Daekyoung Jung, Minsik Oh, Bohyoung Kim^{* (corresponding author)}, Robert J. Freishtat, Mamta Giri, Eric Hoffman, Jinwook Seo^{* (corresponding author)}

Methods2017International journalSCIEIF 3.6

Literature-based condition-specific miRNA-mRNA target prediction

Minsik Oh^{† (first author)}, Sungmin Rhee, Ji Hwan Moon, Heejoon Chae, Sunwon Lee, Jaewoo Kang, Sun Kim^{* (corresponding author)}

PLOS ONE2017International journalSCIEIF 2.8